Abstract LB058: A transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer
Authors: Gaia Grasso, Elisa Marriella, Martina Miotto, Kristi Buzo, Nicole M. Reilly, Pietro Andrei, Pietro P. Vitiello, Giovanni Crisafulli, Sabrina Arena, Giuseppe Rospo, Giorgio Corti, Annalisa Lorenzato, Carlotta Cancelliere, Ludovic Barault, Giulia Gionfriddo, Michael Linnebacher, Mariangela Russo, Federica Di Nicolantonio, Alberto Bardelli
Journal: Cancer Research (2023)

Abstract The number of effective therapies approved for metastatic colorectal cancer (mCRC) is still limited and multiple strategies are continuously explored to expand the drug target repertoire. Among these, the identification of overexpressed genes has prompted the discovery of actionable oncogenic dependencies in multiple tumour types. Starting from RNA sequencing data, we identified transcriptome-wide gene expression outliers, defined as samples showing abnormal expression for a particular gene, across 226 CRC cell lines, considering both overexpression and underexpression events as positive or negative outliers. Then, the distance of each outlier from gene-specific reference points, absolute expression values and differential expression values were considered in a multi-filter strategy to select extreme gene expression outliers, with the hypothesis that they are more likely to be functionally relevant in cancer cells. We also profiled genetic and epigenetic features of CRC cell lines based on whole exome sequencing and DNA methylation microarray data. Extreme positive and negative gene expression outliers were found for 3,533 and 965 genes, respectively, and only some of them were associated with underlying genetic and epigenetic alterations. Gene expression alterations with known therapeutic or diagnostic value in CRC were pinpointed as extreme positive and negative outliers thus confirming the validity of the approach. Annotation of overexpressed enzyme genes according to the Target Development Level (TDL) classification revealed numerous enzymes for which inhibitors are already available. We next explored underexpression events to identify potential synthetic lethal targets. Intriguingly, we found that CRC models lacking expression of the MTAP gene were sensitive to treatment with an inhibitor of the PRMT5:MTA complex currently under clinical development. We found that mapping extreme and transcriptome-wide positive and negative gene expression outliers in CRC cell lines is an effective strategy to identify putative drug targets and biomarkers, independently from the underlying genetic or epigenetic alterations. We indeed present a comprehensive atlas of CRC extreme gene expression outliers which includes events with diagnostic or therapeutic relevance. This resource could also serve as a reference for further discoveries in CRC and other tumour types. Citation Format: Gaia Grasso, Elisa Marriella, Martina Miotto, Kristi Buzo, Nicole M. Reilly, Pietro Andrei, Pietro P. Vitiello, Giovanni Crisafulli, Sabrina Arena, Giuseppe Rospo, Giorgio Corti, Annalisa Lorenzato, Carlotta Cancelliere, Ludovic Barault, Giulia Gionfriddo, Michael Linnebacher, Mariangela Russo, Federica Di Nicolantonio, Alberto Bardelli. A transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB058.